Students will submit their homework to their hand-in folder in the course folder on Collab. You can access this with the map-network-drives command in linux. Then look at ~/Collab/Courses/cs/coursenumber/Student Work/ This folder contiains a directory for each student, and each student's personal folder contains hand-in and return folders.
When you start grading an assignment, copy that assignment from the hand-in folder to the return folder for each student. This provides a permanent record of the particular version of the file that you graded in case there are later disputes.
If you need to make changes to a student's submitted work (including compiling source code), again copy the files to a working folder somewhere in your home directory.
It works well to write out a text file of comments for each student (again somewhere in your home directory). Then, when you're finished grading, copy the comments to each student's return folder. A shell script like this can make this really easy.
Often, instructors will also want a copy of all the comment files. The easiest way to do this is to create a tarball archive and attach it to an e-mail. Run the following command from the directory with the comment files. (Assuming that your comment files are the only text files in the directory).
> tar -cvzf comments.tgz *.txt
It is helpful to students to receive an e-mail telling them to check the return folder once an assignment is graded. You can ask the professor to give you access to the course mailing list for this reason.